New microsatellite loci in the dwarf yams Dioscorea group Epipetrum (Dioscoreaceae)

? Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of two taxa of the Chilean Epipetrum group of Dioscorea to assess their levels of genetic diversity and population differentiation. ? Methods and Results: Eleven microsatellite loci were identified. Six out of nine microsatellites from D. biloba amplified in D. humilis, and the two microsatellites from D. humilis amplified in both taxa. Two different sets of eight loci amplified in each of the two tested taxa, D. biloba and D. humilis. The average number of alleles was 5.75 and 5 for D. biloba and D. humilis, respectively. Higher levels of mean genetic diversity were found in D. biloba (H(E) = 0.639) than in D. humilis (H(E) = 0.414). ? Conclusions: These microsatellite primers will be useful in population genetic studies and to establish conservation strategies in the endangered taxa of the Epipetrum group of Dioscorea.     

Characterization of microsatellite loci from Litsea hypophaea (Lauraceae), a tree endemic to Taiwan

? Premise of the study: Microsatellite primers were developed for the endemic tree Litsea hypophaea (Lauraceae) in Taiwan to investigate its genetic diversity and population genetic structure and to investigate species delimitation within Litsea. ? Methods and Results: Fifteen new simple sequence repeat markers were developed from L. hypophaea with a magnetic bead enrichment method. Most loci were also amplified from three closely related species, L. coreana, L. lii, and L. acutivena. The number of alleles and observed and expected heterozygosities across loci varied with a range of 1-25, 0.000-1.000, and 0.000-0.956, respectively. ? Conclusions: The application of these microsatellite markers of L. hypophaea provides a tool for understanding genetic diversity and population differentiation. In addition, interspecific amplification suggests that these markers will also be useful for species identification of related taxa within Litsea in Taiwan.     

Microsatellite primers in Rhamnus cathartica (Rhamnaceae) and applicability in related taxa to assess hybridization events

? Premise of the study: Microsatellite primers were developed in the introduced shrub Rhamnus cathartica L., to investigate potential hybridization events with related taxa as a stimulus of invasive spread. ? Methods and Results: Using a non-radioactive protocol, 15 primer sets were identified in North American and European populations of R. cathartica. The primers amplified di-, tri- and pentanucelotide repeats with 1-14 alleles per locus. Most primers also amplified in R. lanceolata, R. smithii, and/or Frangula alnus (previously R. frangula). ? Conclusions: These results indicate the utility of primers in R. cathartica for future genetic studies as well as their potential applicability in other related taxa.     

Microsatellite primers in the endangered quillwort Isoetes hypsophila (Isoetaceae) and cross-amplification in I. sinensis

? Premise of the study: The first microsatellite primers were developed for Isoetes hypsophila, an endangered quillwort species endemic to the Qinghai-Tibetan Plateau in China, to further describe its genetic variability and population structure. We also examined their cross-amplification in a congeneric species, I. sinensis. ? Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining Repeats (FIASCO) protocol, nine microsatellite loci were isolated and characterized in 32 samples from four natural populations of I. hypsophila. The primers amplified di- and hexanucleotide repeats with three to 11 alleles per locus. Seven of nine primers were cross-amplified in I. sinensis with two to seven alleles per locus. ? Conclusion: The microsatellite loci primers will be useful for studies of genetic diversity and gene flow in natural populations of Isoetes species.     

Conservation genetics of an island-endemic lizard: low Ne and the critical role of intermediate temperatures for genetic connectivity

Island populations are at higher risk of extinction than mainland populations. Therefore, understanding the factors that facilitate connectivity is particularly pressing for the conservation of island taxa. Sceloporus occidentalis becki, the Island Fence Lizard, is an endemic taxon restricted to the Northern Channel Islands, part of a nearshore archipelago in Southern California, USA. Since the Last Glacial Maximum, fence lizard habitat on the Northern Channel Islands has decreased with rising sea levels and increasing temperatures that have reduced the availability of woody vegetation. More recently, the introduction (and subsequent removal) of invasive ungulates over the last 170 years and recovery of vegetation has resulted in further dramatic habitat modification. Given the potential for genetic bottlenecks, the history of habitat alteration, and topographic and landscape complexity, we used landscape and population genetic approaches to characterize patterns of genetic diversity and structure of Island Fence Lizards on Santa Cruz Island, the largest of the Northern Channel Islands. Our analyses revealed shallow population structure across the island, low effective population size (N_e?=??~?200), and evidence for a recent genetic bottleneck. Landscape genetic analyses showed that connectivity is facilitated by tree canopy cover and shrubland, as well as by intermediate temperatures, emphasizing the importance of woody vegetation and habitats with variable thermal regimes as the climate warms. Combined, these population and landscape genetic analyses suggest that the Island Fence Lizard is of greater conservation concern than currently appreciated, and increased conservation management focus is warranted for this island endemic.

     

The population genetics of nonmigratory Allen’s Hummingbird (Selasphorus sasin sedentarius) following a recent mainland colonization

Allen''s Hummingbird comprises two subspecies, one migratory (Selasphorus sasin sasin) and one nonmigratory (S. s. sedentarius). The nonmigratory subspecies, previously endemic to the California Channel Islands, apparently colonized the California mainland on the Palos Verdes Peninsula some time before 1970 and now breeds throughout coastal southern California. We sequenced and compared populations of mainland nonmigratory Allen''s Hummingbird to Channel Island populations from Santa Catalina, San Clemente, and Santa Cruz Island. We found no evidence of founder effects on the mainland population. Values of nucleotide diversity on the mainland were higher than on the Channel Islands. There were low levels of divergence between the Channel Islands and the mainland, and Santa Cruz Island was the most genetically distinct. Ecological niche models showed that rainfall and temperature variables on the Channel Islands are similar in the Los Angeles basin and predicted continued expansion of nonmigratory Allen''s Hummingbird north along the coast and inland. We also reviewed previous genetic studies of vertebrate species found on the Channel Islands and mainland and showed that broad conclusions regarding island–mainland patterns remain elusive. Challenges include the idiosyncratic nature of colonization itself as well as the lack of a comprehensive approach that incorporates similar markers and sampling strategies across taxa, which, within the context of a comparative study of island–mainland relationships, may lead to inconsistent results.     

High levels of genetic polymorphism in the insular endemic herb Jepsonia malvifolia.

Jepsonia malvifolia is a long-lived perennial herb endemic to the Channel Islands of southern California and Guadalupe Island, Mexico. Twelve populations of J. malvifolia on San Clemente Island were surveyed for their genotype at 21 allozyme loci, revealing high levels of genetic polymorphism. For all individuals across San Clemente Island, 95.2% of loci are polymorphic with A(p) = 2.90 and H(e) = 0.179. Populations averaged 60.2% polymorphic loci with A(p) = 2.42 and H(e) = 0.158. Most variation is found within rather than among populations (G(ST) = 0.101), although differentiation among populations is significant. Genetic identities range from 0.936 to 0.999 with mean I = 0.975. There is no significant relationship between genetic and geographic distance. Gene flow among populations is Nm = 9.5 based on private alleles and Nm = 2.2 based on F(ST). Outcrossing rates based on fixation indices average t = 0.753, indicating a primarily outcrossed mating system. The genetic variation observed is unusually high for an insular endemic herb and indicates that J. malvifolia is unlikely to be endangered by genetic factors.     

Microsatellite markers in the tree peony, Paeonia suffruticosa (Paeoniaceae)

? Premise of the study: Microsatellite primers were developed in the tree peony, Paeonia suffruticosa, to perform paternity tests as well as assignment to variety in special Austrian collections. ? Methods and Results: Using SSR-enriched libraries and EST-mining, 8 polymorphic primer sets were identified in Austrian collections of Paeonia sect. Moutan DC. The primers amplified di- and trinucleotide repeats with 2-6 alleles per locus. All primers also amplified in P. ostii, P. pontaninii var. trolloides, P. delavayi, and P. lutea, and in the herbaceous species P. peregrina and P. tenuifolia (Paeonia sect. Paeon). ? Conclusions: These results show the usefulness of primers in P. suffruticosa for population genetic studies and their ability to cross amplify in related taxa across the genus.     

Isolation and characterization of microsatellite loci in Ainsliaea faurieana (Asteraceae), an endemic plant species on Yakushima Island, Japan, and cross-species amplification in closely related taxa

Fourteen microsatellite loci were isolated and characterized for Ainsliaea faurieana, an endemic perennial plant species on Yakushima Island. In an analysis of 37 individuals from Yakushima Island, the observed number of alleles ranged from two to six. The expected and observed heterozygosities were 0.109-0.811 and 0.000-0.27, respectively. The inbreeding coefficient was 0.489-1.000. The interspecific applicability of these microsatellites was evaluated by analysing three closely related taxa from the Ryukyu Islands. All primer pairs for the 14 loci tested successfully amplified in all taxa.     

Development and characterization of microsatellite markers for Emmenopterys henryi (Rubiaceae), a rare tree from China

? Premise of the study: Compound microsatellite primers were developed for Emmenopterys henryi, an endangered deciduous tree endemic to China, to assess its genetic diversity and population structure as well as its evolutionary history. ? Methods and Results: Using the compound microsatellite marker technique, 10 pairs of polymorphic microsatellite primers were isolated and characterized in E. henryi. Levels of polymorphism were tested across a total of 63 individuals from three natural populations. Allele numbers varied from 10 to 20 per locus, with an average of 14.50 alleles per locus. The observed heterozygosity per locus ranged from 0.125 to 0.962, and the expected heterozygosity ranged from 0.377 to 0.903. ? Conclusions: The highly polymorphic markers developed and characterized in this study will facilitate evolutionary and population genetic studies in E. henryi.     

Narrow water barriers prevent multiple colonizations and limit gene flow among California Channel Island wild buckwheats (Eriogonum: Polygonaceae)

The relative roles of chance colonization and subsequent gene flow in the development of insular endemic biotas have been extensively studied in remote oceanic archipelagos, but are less well characterized on nearshore island systems. The current study investigated patterns of colonization and divergence between and within two wild buckwheat species (Polygonaceae), Eriogonum arborescens and E. giganteum, endemic to the California Channel Islands to determine whether geographical isolation is driving diversification. Using plastid and nuclear sequence data and microsatellite allele frequencies, we determined that gene flow in these Eriogonum spp. is restricted by isolation. The data suggest that successful colonization of and gene flow among the islands are infrequent. Colonization appears to have followed a stepping‐stone model that is consistent with a north‐to‐south pattern across the islands. This colonization pattern coupled with relatively little post‐colonization inter‐island gene flow, particularly among southern islands, has generated a pattern of more divergent lineages on the isolated southern islands. These results run counter to the general expectation that all islands close to a continental source should receive a high level of gene flow. Finally, management recommendations focused on protecting the lineages from loss of private alleles and the erosion of the remaining genetic diversity are offered.     

Population structure of loggerhead shrikes in the California Channel Islands

The loggerhead shrike (Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity.     

Development of intron targeting (IT) markers for potato and cross-species amplification in Solanum nigrum (Solanaceae)

? Premise of the study: Intron Targeting (IT) primers were developed for potato using expressed sequence tags (EST) and NCBI database records to study genetic diversity. ? Methods and Results: Twenty-nine polymorphic intron targeting (IT) markers were generated and characterized from 30 samples of potato and 22 samples of Solanum nigrum to detect polymorphism. The number of alleles (A) per locus ranged from 2 to 7 in the analyzed populations, and the observed heterozygosity (H(O)) and expected heterozygosity (H(E)) from 0 to 0.833 and 0.750, respectively. All of the primers also amplified in the related species S. nigrum. ? Conclusions: The developed markers will provide valuable tools for genetic diversity analysis, genetic mapping, and marker-assisted breeding of potato and related Solanum species.     

Genetic Divergence of an Avian Endemic on the Californian Channel Islands

The Californian Channel Islands are near–shore islands with high levels of endemism, but extensive habitat loss has contributed to the decline or extinction of several endemic taxa. A key parameter for understanding patterns of endemism and demography in island populations is the magnitude of inter–island dispersal. This paper estimates the extent of migration and genetic differentiation in three extant and two extinct populations of Channel Island song sparrows (Melospiza melodia graminea). Inter–island differentiation was substantial (G''''_ST: 0.14–0.37), with San Miguel Island having the highest genetic divergence and lowest migration rates. Santa Rosa and Santa Cruz Island populations were less diverged with higher migration rates. Genetic signals of past population declines were detected in all of the extant populations. The Channel Island populations were significantly diverged from mainland populations of M. m. heermanni (G''''_ST: 0.30–0.64). Ten mtDNA haplotypes were recovered across the extant and extinct Channel Island population samples. Two of the ten haplotypes were shared between the Northern and Southern Channel Islands, with one of these haplotypes being detected on the Californian mainland. Our results suggest that there is little contemporary migration between islands, consistent with early explanations of avian biogeography in the Channel Islands, and that song sparrow populations on the northern Channel Islands are demographically independent.     

Microsatellite markers from Ceanothus roderickii (Rhamnaceae) using next-generation sequencing technology

? Premise of the study: Ceanothus roderickii is an endangered shrub endemic to California. To investigate the population genetics of this species, including the genetic consequences of population fragmentation and hybridization, 10 microsatellite markers were developed. ? Methods and Results: Using next-generation sequencing (454) data from a single C. roderickii individual, 10 microsatellite markers were developed. A group of 12 individuals representing all of the major C. roderickii populations were analyzed. All loci were found to be polymorphic, with a range from two to 12 alleles per locus. Observed heterozygosity ranged from 0.08 to 0.83 across loci. All 10 loci were also amplifiable in at least one other Ceanothus species. ? Conclusions: Results presented here indicate the utility of our new microsatellite primers in ongoing and future studies concerning population genetics and gene flow in C. roderickii, as well as the potential applicability of these primers in similar studies on other Ceanothus species.     

Characterization of polymorphic microsatellite markers in the water rat (Hydromys chrysogaster)

The water rat (Hydromys chrysogaster) is well adapted to a semiaquatic life and is endemic to dispersed regions of Australia and New Guinea. To analyse the genetic diversity of water rat populations, polymorphic microsatellite markers were developed. A partial genomic library was screened for microsatellite sequences. Following isolation of the microsatellite sequences, primers were designed to amplify seven loci and of these loci, five were polymorphic. The sample tested for polymorphisms came from areas across Australia and New Guinea. Between three and 13 alleles were detected for each locus. In addition the primers amplified two loci in Mus musculus and Rattus rattus.     

The Transferability of SSR Markers in Seven Asteraceae Species to Taxa in the Natural Hybrid Zone between Ligularia duciformis and Lparadoxa

Ligularia × maoniushanensis (Asteraceae) is a natural hybrid species of Lduciformis and Lparadoxa. In order to study hybridization and genetic structure of taxa in the hybrid zones between Lduciformis and Lparadoxa, cross species SSR primers were screened using 94 individuals of two hybrid zones’ hybrids and its parents from 145 nuclear SSR primers which had been developed from Ligularia, Farfugium, Senecio and Helianthus. The results indicated that 54 loci were successfully amplified at least one taxon of three taxa. A total of 17 loci were successfully amplified at three taxa, of which 11 were polymorphic in L. × maoniushanensis, and the number of alleles (NA) ranged from 2 to 14 (average 48) and the ranges of observed (HO) and expected (HE) heterozygosities were 0053~1000 and 0051~0887, respectively. Of which 9 were polymorphic in Lduciformis, and the number of alleles (NA) ranged from 3 to 12 (average 74) and the ranges of observed (HO) and expected (HE) heterozygosities were 0200~0971 and 0283~0844, respectively. Of which 10 were polymorphic in Lparadoxa, the number of alleles (NA) ranged from 4 to 15 (average 7.6) and the ranges of observed (HO) and expected (HE) heterozygosities were 0025~0974 and 0097~0846, respectively. The results will facilitate the further analysis of genetic structure and hybrid extent about taxa in hybrid zone between Lduciformis and Lparadoxa.     

Microsatellite development for an endangered riparian inhabitant, Lilaeopsis schaffneriana subsp. recurva (Apiaceae)

? Premise of the study: Microsatellite markers were developed and characterized to evaluate genetic diversity and population structure in Lilaeopsis schaffneriana subsp. recurva, an endangered species endemic to wetlands dispersed throughout southeastern Arizona, USA, and northern Sonora, Mexico. ? Methods and Results: Eight loci (one of which was monomorphic) were developed and characterized in 48 individuals from two populations. The total number of alleles was 35, ranging from one to 10 per locus. Many of the primers amplified in L. carolinensis, L. chinensis, L. masonii, L. occidentalis, L. schaffneriana subsp. schaffneriana, Oxypolis fendleri, and Eryngium lemmonii. ? Conclusions: Development of these novel microsatellite loci will facilitate a deeper understanding of genetic diversity, mode of reproduction, and population structure not only in L. schaffneriana subsp. recurva, but also in apiaceous relatives.     

Characterization of microsatellite loci in Festuca gautieri (Poaceae) and transferability to F. eskia and F. xpicoeuropeana

? Premise of the study: Enriched genomic libraries were used to isolate and characterize microsatellite loci in Festuca gautieri, an important plant component of subalpine calcareous grasslands of the eastern Iberian Peninsula, the Pyrenees, and the Cantabrian Mountains. Microsatellites were required to investigate landscape genetics across its distribution range and at a narrower geographical scale within the Ordesa y Monte Perdido, Aigüestortes, and Picos de Europa Spanish national parks. ? Methods and Results: Ten polymorphic microsatellite loci were characterized. They amplified a total of 116 alleles in a sample of 30 individuals of F. gautieri, showing high levels of genetic diversity (expected heterozygosity = 0.821). Cross-species transferability to two other close congeners, F. eskia and F ×picoeuropeana, increased the total number of alleles to 137. These taxa showed lower numbers of alleles but similar levels of genetic diversity to F. gautieri. ? Conclusions: These microsatellite primers will be useful in population and landscape genetics and in establishing conservation strategies for these characteristic elements of subalpine pastures.     

Microsatellite markers for the endangered root holoparasite Dactylanthus taylorii (Balanophoraceae) from 454 pyrosequencing

? Premise of the study: Microsatellite loci were isolated and developed as polymorphic markers for the New Zealand endemic root holoparasite Dactylanthus taylorii for use in population and conservation genetics studies. ? Methods and Results: Shotgun 454 pyrosequencing was performed on genomic DNA pooled from three individuals of D. taylorii. From 61709 individual sequence reads, primers for 753 microsatellite loci were developed in silico and 72 of these were tested for consistent amplification and variability. Ten microsatellite loci were found to be polymorphic and consistently scorable when screened in 44 individuals from five geographically distant populations. The number of alleles per locus ranged from four to 16 with an average of 9.7, and average observed heterozygosity per locus was between 0.182 and 0.634. ? Conclusions: These polymorphic microsatellite markers establish an important resource for ongoing conservation initiatives and planned population genetic studies of D. taylorii.